cumulativeCTSSdistribution: Calculating cumulative sum of CAGE signal along genomic...

In ge11232002/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

Calculates cumulative sum of CAGE signal along each tag cluster or consensus cluster in every CAGE dataset within CAGEset object.

Usage

cumulativeCTSSdistribution(object, clusters, useMulticore = FALSE, 
                           nrCores = NULL)

Arguments

object	A CAGEset object
clusters	Which clusters should be used. Can be either clusters = "tagClusters" to calculate cumulative sum along tag clusters (different set of genomic coordinates for every CAGE experiment) or clusters = "consensusClusters" to calculate cumulative sum along consensus clusters (same set of genomic coordinates for every CAGE experiment).
useMulticore	Logical, should multicore be used. useMulticore = TRUE is supported only on Unix-like platforms.
nrCores	Number of cores to use when useMulticore = TRUE. Default value NULL uses all detected cores.

Value

The slot CTSScumulativesTagClusters (when clusters = "tagClusters") or CTSScumulativesConsensusClusters (when clusters = "consensusClusters") of the provided CAGEset object will be occupied by the list containing cumulative sum of the CAGE signal along genomic regions per CAGE experiment.

Author(s)

Vanja Haberle

Examples

load(system.file("data", "exampleCAGEset.RData", package="CAGEr"))

cumulativeCTSSdistribution(object = exampleCAGEset, clusters = "tagClusters")

ge11232002/CAGEr documentation built on May 17, 2019, 12:13 a.m.